Mummichog pathway and network analysis for metabolomics

Mummichog is a free Python program for analyzing data from high throughput, untargeted metabolomics.
It leverages the organization of metabolic networks to predict functional activity directly from feature tables, bypassing metabolite identification. Thus, high-quality hypotheses can be quickly generated from a LC-MS data table.

Jupyter notebooks are to data people like lab notebooks to bench scientists. They keep code and result in the same web browser. It's increasinlgy popular for data analysis and collaboration. We continue posting notebooks as tutorials and for record keeping.

A common error, "AttributeError: 'NodeView' object has no attribute 'sort’", is caused by Networkx 2.x, which is not backward compatible. This can be fixed by installing Networkx 1.x via pip in your terminal, "sudo pip install networkx==1.10".

Emory University Sys/Bio/Info Group runs a monthly meeting on Systems Biology and Bioinformatics. These are casual seminars and discussions, on every first Wednesday of the month, 12 pm, Whitehead Biomedical Research Building, Rm 200. Email Dr. Shuzhao Li to join the mailing list.